update figure printing

Author: Remi-Gau

demos/MoAE/MoAEpilot_run.m

@@ -43,6 +43,7 @@
 bidsCopyRawFolder(opt, 1);
 
 % In case you just want to run segmentation and skull stripping
+% Skull stripping is also included in 'bidsSpatialPrepro'
 % bidsSegmentSkullStrip(opt);
 
 bidsSTC(opt);

docs/source/method_section_boilerplate.rst

@@ -1,12 +1,6 @@
 Boilerplate methods section
 ***************************
 
-Use the report function to get a print out of the content of a dataset.
-
-.. automodule:: src.reports 
-
-.. autofunction:: reportBIDS
-
 Preprocessing
 =============
 
@@ -83,3 +77,13 @@ Friston KJ, Ashburner J, Frith CD, Poline J-B, Heather JD & Frackowiak RSJ
 Corbin, N., Todd, N., Friston, K. J. & Callaghan, M. F. Accurate modeling of
 temporal correlations in rapidly sampled fMRI time series. Hum. Brain Mapp. 39,
 3884–3897 (2018).
+
+
+---
+
+Use the report function to get a print out of the content of a dataset.
+
+.. automodule:: src.reports 
+
+.. autofunction:: reportBIDS
+.. autofunction:: copyGraphWindownOutput

src/defaults/spm_my_defaults.m

@@ -9,6 +9,10 @@
 
   global defaults
 
+  % User Interface defaults
+  % ==========================================================================
+  defaults.ui.print   = 'png';
+
   % File format specific
   % ==========================================================================
   defaults.mat.format     = '-v7';

src/reports/copyGraphWindownOutput.m

@@ -0,0 +1,61 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
+function imgNb = copyGraphWindownOutput(opt, subID, action, imgNb)
+  %
+  % Looks into the current directory for an ``spm_.*imgNb.png`` file and moves it into
+  % the output directory ``sub-label/figures``.
+  % The output name of the file is
+  % ``yyyymmddHHMM_sub-label_task-label_action.png``
+  %
+  % USAGE::
+  %
+  %   imgNb = copyGraphWindownOutput(opt, subID, [action = '',] [imgNb = 1])
+  %
+  % :param opt: options
+  % :type opt: structure
+  % :param subID:
+  % :type subID: string
+  % :param action:
+  % :type action: string
+  % :param imgNb: image number to look for. SPM increments them automatically.
+  % :type imgNb: integer
+  %
+  % :returns: - :imgNb: (integer) number of the next image to get.
+  %
+  % assumes that no file was generated if SPM is running in command line mode
+
+  if ~spm('CmdLine')
+
+    if nargin < 4 || isempty(imgNb)
+      imgNb = 1;
+    end
+
+    if nargin < 3 || isempty(action)
+      action = '';
+    end
+
+    figureDir = fullfile(opt.derivativesDir, ['sub-' subID], 'figures');
+    if ~exist(figureDir, 'dir')
+      mkdir(figureDir);
+    end
+
+    file = spm_select('FPList', pwd, sprintf('^spm_.*%i.png$', imgNb));
+
+    if ~isempty(file)
+
+      targetFile = [datestr(now, 'yyyymmddHHMM') ...
+                    '_sub-', subID, ...
+                    '_task-',   opt.taskName, ...
+                    '_' action '.png'];
+
+      movefile( ...
+               file, ...
+               fullfile(figureDir, targetFile));
+
+      imgNb = imgNb + 1;
+
+    end
+
+  end
+
+end

src/utils/copyGraphWindownOutput.m

@@ -1,5 +1,5 @@
 % (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
 
 function [interactiveWindow, graphWindow, cmdLine] = setGraphicWindow()
-    [interactiveWindow, graphWindow, cmdLine] = spm('FnUIsetup');
+  [interactiveWindow, graphWindow, cmdLine] = spm('FnUIsetup');
 end

src/utils/setGraphicWindow.m

@@ -1,4 +1,4 @@
-% (C) Copyright 20120 CPP BIDS SPM-pipeline developpers
+% (C) Copyright 2020 CPP BIDS SPM-pipeline developpers
 
 function bidsSegmentSkullStrip(opt)
   %

src/workflows/bidsSegmentSkullStrip.m

@@ -23,6 +23,8 @@ function bidsSpatialPrepro(opt)
   end
   opt = loadAndCheckOptions(opt);
 
+  setGraphicWindow();
+
   % load the subjects/Groups information and the task name
   [group, opt, BIDS] = getData(opt);
 
@@ -43,14 +45,11 @@ function bidsSpatialPrepro(opt)
 
       printProcessingSubject(groupName, iSub, subID);
 
-      % identify sessions for this subject
-      sessions = getInfo(BIDS, subID, opt, 'Sessions');
-
       matlabbatch = setBatchSelectAnat(matlabbatch, BIDS, opt, subID);
       opt.orderBatches.selectAnat = 1;
 
       action = [];
-      if  strcmp(opt.space, 'individual')
+      if strcmp(opt.space, 'individual')
         action = 'realignUnwarp';
       end
       [matlabbatch, voxDim] = setBatchRealign(matlabbatch, BIDS, subID, opt, action);
@@ -79,6 +78,12 @@ function bidsSpatialPrepro(opt)
 
       spm_jobman('run', matlabbatch);
 
+      imgNb = copyGraphWindownOutput(opt, subID, 'realign');
+      if  strcmp(opt.space, 'individual')
+        imgNb = copyGraphWindownOutput(opt, subID, 'unwarp', imgNb);
+      end
+      imgNb = copyGraphWindownOutput(opt, subID, 'func2anatCoreg', imgNb);
+
     end
   end